The mechanical bond on carbon nanotubes: diameter-selective functionalization and effects on physical properties

We describe the functionalization of SWNTs enriched in (6,5) chirality with electron donating macrocycles to yield rotaxane-type mechanically interlocked carbon nanotubes (MINTs).Investigations by means of TEM and control experiments corroborated the interlocked nature of the MINTs. A comprehensive characterization of the MINTs through UV-vis-NIR, Raman, fluorescence, transient absorption spectroscopy, cyclic voltammetry, and chronoamperometry was carried out.Analyses of the spectroscopic data reveal that the MINT-forming reaction proceeds with diameter selectivity, favoring functionalization of (6,5) SWNTs rather than larger (7,6) SWNTs. In the ground state, we found a lack of significant charge-transfer interactions between the electron donor exTTF and the SWNTs. Upon photoexcitation, efficient charge-transfer between the electron donating exTTF macrocycles and SWNTs was demonstrated. As a complement, we established significantly different charge-transfer rate constants and diffusion coefficients for MINTs and the supramolecular models,which confirms the fundamentally different type of interactions between exTTF and SWNTs in the presence or absence of the mechanical bond. Molecular mechanics and DFT calculations support the experimental findings

Siesta: Recent developments and applications

A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-1990s, SIESTA’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a realspace grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various post-processing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments. Published under license by AIP Publishing.Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280). We also acknowledge Honghui Shang and Xinming Qin for giving us access to the honpas code, where a preliminary version of the hybrid functional support described here was implemented. We are indebted to other contributors to the Siesta project whose names can be seen in the Docs/Contributors.txt file of the Siesta distribution, and we thank those, too many to list, contributing fixes, comments, clarifications, and documentation for the code.Peer reviewe

Siesta: Recent developments and applications

A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta?s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin?orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.SIESTA development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-

Propriétés structurales et électroniques d'agrégats CuOn (n=1-6) et du composé solide Cu2(OH)3(NO3) : une étude par la fonctionnelle de densité

Rapporteurs : Pr H. Dreyssé, Pr X. Gonze, Pr P. Gressier / Examinateur : Dr M.M. Rohmer / Invité : Dr M. DrillonThe structural and electronic properties of small CuO clusters, and the magnetic properties of copper hydroxonitrate, have been determined within the density functional theory (DFT) framework by means of ab initio molecular dynamics. The calculations on the clusters have been carried out within the local spin-polarized density approximation (LSDA) with use of a generalized gradient correction (GGA). The wavefunctions have been projected on a plane-wave basis set, combined with periodic boundary conditions. Ultrasoft pseudopotentials have also been used. The equilibrium geometries of the clusters --- experimentally unreachable --- have been first determined, both for neutral and anionic clusters, in two different spin states for each of them. Temperature effects have been taken into account with help of finite-temperature ab initio molecular dynamics simulations. A specific method has been developed to characterize the electronic properties of these clusters. A series of electronic structure calculations has been done on copper hydroxinitrate, for different supercell sizes. This time norm-conserving Troullier-Martins pseudopotentials have been used. The spin density within copper and oxygen atoms has been analysed for every system. The principles ruling its repartition have been determined, the magnetic-coupling constants have been tentatively evaluated, and the influence of the supercell size has been traced.Les propriétés structurales et électroniques de petits agrégats CuO, d'une part, et les propriétés magnétiques de l'hydroxynitrate de cuivre, d'autre part, ont été déterminées dans le cadre de la théorie de la fonctionnelle de densité (DFT), à l'aide de la dynamique moléculaire ab initio. Les calculs concernant les agrégats ont été effectués dans l'approximation de densité locale polarisée en spin (LSDA), avec une correction de gradient généralisé (GGA). Les fonctions d'onde ont été projetées sur une base d'ondes planes associée à des conditions aux limites périodiques. Des pseudopotentiels de Vanderbilt ont été utilisés. Les géométries d'équilibre des agrégats, inaccessibles expérimentalement, ont tout d'abord été déterminées, à la fois pour des agrégats neutres et négativement chargés, dans deux états de spin différents pour chacun. Les effets de la température ont été pris en compte à l'aide de simulations de dynamique moléculaire ab initio à température finie. Une méthode spécifique a été développée pour caractériser les propriétés électroniques de ces agrégats. Une série de calculs de structure électronique a été menée sur l'hydroxynitrate de cuivre, pour différentes tailles de la cellule de simulation. Les calculs ont cette fois fait appel à des pseudopotentiels à norme conservée de Troullier-Martins. La densité de spin au niveau des atomes de cuivre et d'oxygène a été analysée pour chaque système étudié. Les principes gouvernant sa répartition ont été dégagés, une tentative d'évaluation des constantes de couplage a été effectuée et l'influence de la taille de la cellule a été considérée

Collaborative software development for nanoscale physics

Trabajo presentado a la 13e édition des Rencontres Mondiales du Logiciel Libre, celebrad en Geneve (Suiza) del 7 al 12 de Julio de 2012.ETSF/Nanoquanta Research Network; ETSF EU Project (contract 211956); UPV/EHU: contract PIC-28-12 (2012); MICINN/MINECO: contract PTA-2008-0982-I (2009-2011), MEC: project FIS2007-65702-C02-01 (2009-2011) and Gobierno Vasco: projects IT-319-07 + ETORTEK-inanoGUNE (2009-2011).Peer reviewe

Propriétés structurales et électroniques d'agrégats CuOn (n=1-6) et du composé solide Cu2(OH)3(NO3) (une étude par la fonctionnelle de densité)

Les propriétés structurales et électroniques de petits agrégats CuO,d'une part, et les propriétés magnétiques de l'hydroxynitrate de cuivre, d'autre part, ont été déterminées dans le cadre de la théorie de la fonctionnelle de densité (DFT), à l'aide de la dynamique moléculaire ab initio.Les calculs concernant les agrégats ont été effectués dans l'approximation de densité locale polarisée en spin (LSDA), avec une correction de gradient généralisé (GGA). Les fonctions d'onde ont été projetées sur une base d'ondes planes associe e à des conditions aux limites périodiques. Des pseudopotentiels de Vanderbilt ont été utilisés.Les géométries d'équilibre des agrégats, inaccessibles expérimentalement,ont tout d'abord été déterminées, à la fois pour des agrégats neutres et négativement chargés, dans deux états de spin différents pour chacun.Les effets de la température ont été pris en compte à l'aide de simulations de dynamique moléculaire ab initio à température finie. Une méthode spécifique a été développée pour caractériser les propriétés électroniques de ces agrégats.Une série de calculs de structure électronique a été menée sur l'hydroxynitrate de cuivre, pour différentes tailles de la cellule de simulation. Les calculs ont cette fois fait appel à des pseudopotentiels à norme conservée de Troullier-Martins.La densité de spin au niveau des atomes de cuivre et d'oxygène a été analysée pour chaque système étudié. Les principes gouvernant sa répartition ont été dégagés, une tentative d'évaluation des constantes de couplage a été effectuée et l'influence de la taille de la cellule a été considérée.The structural and electronic properties of small CuO clusters, and the magnetic properties of copper hydroxonitrate, have been determined within the density functional theory (DFT) framework by means of ab initio molecular dynamics.The calculations on the clusters have been carried out within the local spin-polarized density approximation (LSDA) with use of a generalized gradient correction (GGA). The wavefunctions have been projected on a plane-wave basis set, combined with periodic boundary conditions. Ultrasoft pseudopotentials have also been used. The equilibrium geometries of the clusters experimentally unreachable have been first determined, both forneutral and anionic clusters, in two different spin states for each of them. Temperature effects have been taken into account with help of finite-temperature ab initio molecular dynamics simulations. A specific method has been developed to characterize the electronicproperties of these clusters.A series of electronic structure calculations has been done on copper hydroxonitrate, for different supercell sizes. This time norm-conservingTroullier-Martins pseudopotentials have been used.The spin density within copper and oxygen atoms has been analysed for every system. The principles ruling its repartition have been determined, the magnetic-coupling constants have been tentatively evaluated, and the influenceof the supercell size has been tracedSTRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

The psml format and library for norm-conserving pseudopotential data curation and interoperability

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with Siesta and Abinit, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability.Comment: 39 pages, 2 figure

Paving the way towards Abinit 8 in the post-Moore’s law era

Trabajo presentado al 6th International ABINIT Developer Workshop celebrado en Dinard (Francia) del 15 al 18 de Abril de 2013.-- et al.Peer reviewe

Harnessing the power of modern package management tools for a large Fortran-90-based project: the mutation of ABINIT

ABINIT is a Fortran 90 free software application that allows the atomic-scale simulation of properties of matter, thanks to Density Functional Theory and Many-Body Perturbation Theory. It is used by more than thousand individuals, who enjoy the wide spectrum of properties that ABINIT allows to compute easily. Several dozen developers contribute to ABINIT from different parts of the world. In 2004, it was perceived that a change of the paradigm for source and package management was needed, in order to benefit from standard package management tools. Thus started a noticeable mutation of ABINIT. Although the restructuration of the Fortran 90 source directories was needed, the biggest clarification arose from understanding the different kinds of people linked to ABINIT, i.e. end-users, developers and maintainers, and the parts of the package they should have access to or control of. Previously, everyone was modifying the source and build system, while further advances required more specialisation in the community, e.g. the management of external libraries, in growing number, which has to be done by skilled maintainers. To address the issues raised by Fortran compilers, and because the ABINIT developers are mostly scientists, it was decided to provide support beyond the GNU Autotools (nowadays the paradigm for binary/package generation) by developing a new build system on top of it. While building ABINIT is now much simpler for end-users, we have had to deal carefully with the additional complexity encountered by developers and maintainers. We discuss the issues that appeared during the mutation. All these efforts now guarantee further extensibility and maintainability of ABINIT, and have nicely improved its visibility in different communities, with the integration of the packages into the Debian, Gentoo and Ubuntu Linux distributions. Being generic and portable, the new build system might be used in the future by other projects as well